diff --git a/src/binary_c_python.c b/src/binary_c_python.c
index d5b062972d76a3c7d5c989446dfccdd66d111610..f433267b590d87b77d49eefbd8aa3f4ed41ce410 100644
--- a/src/binary_c_python.c
+++ b/src/binary_c_python.c
@@ -543,3 +543,569 @@ static PyObject* binary_c_free_store_memaddr(PyObject *self, PyObject *args)
return Py_BuildValue("");
}
+
+
+
+#include "binary_c_python.h"
+#include <time.h>
+#include <sys/timeb.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <stdint.h>
+
+/* Binary_c python API
+ * Set of c-functions that interface with the binary_c api.
+ * These functions are called by python, first through binary_c_python.c,
+ * and there further instructions are given on how to interface
+ *
+ * Contains several functions:
+ * // evolution
+ * run_system
+
+ * // utility
+ * return_arglines
+ * return_help_info
+ * return_help_all_info
+ * return_version_info
+
+ * // other
+ * create_store
+ *
+ */
+
+// #define _CAPTURE
+#ifdef _CAPTURE
+static void show_stdout(void);
+static void capture_stdout(void);
+#endif
+
+/* global variables */
+int out_pipe[2];
+int stdoutwas;
+
+/* =================================================================== */
+/* Functions to evolve systems */
+/* =================================================================== */
+
+/*
+Function that runs a system. Has multiple input parameters:
+Big function. Takes several arguments. See binary_c_python.c docstring.
+TODO: Describe each input
+*/
+int run_system(char * argstring,
+ long int custom_logging_func_memaddr,
+ long int store_memaddr,
+ long int persistent_data_memaddr,
+ int write_logfile,
+ int population,
+ char ** const buffer,
+ char ** const error_buffer,
+ size_t * const nbytes)
+{
+ /* memory for system */
+ struct libbinary_c_stardata_t *stardata = NULL;
+
+ // Store:
+ /* Check the value of the store_memaddr */
+ struct libbinary_c_store_t *store;
+ if(store_memaddr != -1)
+ {
+ // load the store from the integer that has been passed
+ store = (void*)store_memaddr;
+ }
+ else
+ {
+ // struct libbinary_c_store_t * store = NULL;
+ store = NULL;
+ }
+
+ // persistent_data:
+ struct libbinary_c_persistent_data_t *persistent_data;
+ if(persistent_data_memaddr != -1)
+ {
+ // load the persistent data from the long int that has been passed
+ persistent_data = (void*)persistent_data_memaddr;
+ debug_printf("Took long int memaddr %ld and loaded it to %p\n", persistent_data_memaddr, (void*)&persistent_data);
+ }
+ else
+ {
+ persistent_data = NULL;
+ debug_printf("persistent_data memory adress was -1, now setting it to NULL\n");
+ }
+
+ /* Set up new system */
+ binary_c_new_system(&stardata, // stardata
+ NULL, // previous_stardatas
+ NULL, // preferences
+ &store, // store
+ &persistent_data, // persistent_data
+ &argstring, // argv
+ -1 // argc
+ );
+
+ // Add flag to enable
+ /* disable logging */
+ if(write_logfile != 1)
+ {
+ snprintf(stardata->preferences->log_filename,
+ STRING_LENGTH-1,
+ "%s",
+ "/dev/null");
+ snprintf(stardata->preferences->api_log_filename_prefix,
+ STRING_LENGTH-1,
+ "%s",
+ "/dev/null");
+ }
+
+ /* output to strings */
+ stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
+ stardata->preferences->batchmode = BATCHMODE_LIBRARY;
+
+ /* Check the value of the custom_logging_memaddr */
+ if(custom_logging_func_memaddr != -1)
+ {
+ stardata->preferences->custom_output_function = (void*)(struct stardata_t *)custom_logging_func_memaddr;
+ }
+
+ debug_printf("ensemble_defer: %d\n", stardata->preferences->ensemble_defer);
+
+ /* do binary evolution */
+ binary_c_evolve_for_dt(stardata,
+ stardata->model.max_evolution_time);
+
+ /* get buffer pointer */
+ binary_c_buffer_info(stardata, buffer, nbytes);
+
+ /* get error buffer pointer */
+ binary_c_error_buffer(stardata, error_buffer);
+
+ /* Determine whether to free the store memory adress*/
+ Boolean free_store = FALSE;
+ if (store_memaddr == -1)
+ {
+ Boolean free_store = TRUE;
+ }
+
+ /* Determine whether to free the persistent data memory adress*/
+ Boolean free_persistent_data = FALSE;
+ if (persistent_data_memaddr == -1)
+ {
+ debug_printf("Decided to free the persistent_data memaddr\n");
+ Boolean free_persistent_data = TRUE;
+ }
+
+ /* free stardata (except the buffer) */
+ binary_c_free_memory(&stardata, // Stardata
+ TRUE, // free_preferences
+ TRUE, // free_stardata
+ free_store, // free_store
+ FALSE, // free_raw_buffer
+ free_persistent_data // free_persistent
+ );
+
+ return 0;
+}
+
+/* =================================================================== */
+/* Functions to call other API functionality like help and arglines */
+/* =================================================================== */
+
+int return_arglines(char ** const buffer,
+ char ** const error_buffer,
+ size_t * const nbytes)
+{
+ /* memory for N binary systems */
+ struct libbinary_c_stardata_t *stardata = NULL;
+ struct libbinary_c_store_t *store = NULL;
+ char *empty_str = "";
+
+ /* Set up new system */
+ binary_c_new_system(&stardata, // stardata
+ NULL, // previous_stardatas
+ NULL, // preferences
+ &store, // store
+ NULL, // persistent_data
+ &empty_str, // argv
+ -1 // argc
+ );
+
+ /* disable logging */
+ snprintf(stardata->preferences->log_filename,
+ STRING_LENGTH-1,
+ "%s",
+ "/dev/null");
+ snprintf(stardata->preferences->api_log_filename_prefix,
+ STRING_LENGTH-1,
+ "%s",
+ "/dev/null");
+
+ /* output to strings */
+ stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
+ stardata->preferences->batchmode = BATCHMODE_LIBRARY;
+
+ /* List available arguments */
+ binary_c_list_args(stardata);
+
+ /* get buffer pointer */
+ binary_c_buffer_info(stardata,buffer,nbytes);
+
+ /* get error buffer pointer */
+ binary_c_error_buffer(stardata,error_buffer);
+
+ /* free stardata (except the buffer) */
+ binary_c_free_memory(&stardata, // Stardata
+ TRUE, // free_preferences
+ TRUE, // free_stardata
+ TRUE, // free_store
+ FALSE, // free_raw_buffer
+ TRUE // free_persistent
+ );
+
+ return 0;
+}
+
+
+int return_help_info(char * argstring,
+ char ** const buffer,
+ char ** const error_buffer,
+ size_t * const nbytes)
+{
+ struct libbinary_c_stardata_t *stardata = NULL;
+ struct libbinary_c_store_t *store = NULL;
+
+ /* Set up new system */
+ binary_c_new_system(&stardata, // stardata
+ NULL, // previous_stardatas
+ NULL, // preferences
+ &store, // store
+ NULL, // persistent_data
+ &argstring, // argv
+ -1 // argc
+ );
+
+ /* output to strings */
+ stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
+ stardata->preferences->batchmode = BATCHMODE_LIBRARY;
+
+ /* Ask the help api */
+ binary_c_help(stardata, argstring);
+
+ /* get buffer pointer */
+ binary_c_buffer_info(stardata, buffer, nbytes);
+
+ /* get error buffer pointer */
+ binary_c_error_buffer(stardata, error_buffer);
+
+ /* free stardata (except the buffer) */
+ binary_c_free_memory(&stardata, // Stardata
+ TRUE, // free_preferences
+ TRUE, // free_stardata
+ TRUE, // free_store
+ FALSE, // free_raw_buffer
+ TRUE // free_persistent
+ );
+
+ return 0;
+}
+
+
+int return_help_all_info(char ** const buffer,
+ char ** const error_buffer,
+ size_t * const nbytes)
+{
+ struct libbinary_c_stardata_t *stardata = NULL;
+ struct libbinary_c_store_t *store = NULL;
+ char * empty_str = "";
+
+ /* Set up new system */
+ binary_c_new_system(&stardata, // stardata
+ NULL, // previous_stardatas
+ NULL, // preferences
+ &store, // store
+ NULL, // persistent_data
+ &empty_str, // argv
+ -1 // argc
+ );
+
+ /* output to strings */
+ stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
+ stardata->preferences->batchmode = BATCHMODE_LIBRARY;
+
+ /* Ask the help api */
+ binary_c_help_all(stardata);
+
+ /* get buffer pointer */
+ binary_c_buffer_info(stardata, buffer, nbytes);
+
+ /* get error buffer pointer */
+ binary_c_error_buffer(stardata, error_buffer);
+
+ /* free stardata (except the buffer) */
+ binary_c_free_memory(&stardata, // Stardata
+ TRUE, // free_preferences
+ TRUE, // free_stardata
+ TRUE, // free_store
+ FALSE, // free_raw_buffer
+ TRUE // free_persistent
+ );
+
+ return 0;
+}
+
+
+int return_version_info(char ** const buffer,
+ char ** const error_buffer,
+ size_t * const nbytes)
+{
+ struct libbinary_c_stardata_t *stardata = NULL;
+ struct libbinary_c_store_t * store = NULL;
+ char * empty_str = "";
+
+ /* Set up new system */
+ binary_c_new_system(&stardata, // stardata
+ NULL, // previous_stardatas
+ NULL, // preferences
+ &store, // store
+ NULL, // persistent_data
+ &empty_str, // argv
+ -1 // argc
+ );
+
+ /* output to strings */
+ stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
+ stardata->preferences->batchmode = BATCHMODE_LIBRARY;
+
+ /* Ask the help api */
+ binary_c_version(stardata);
+
+ /* get buffer pointer */
+ binary_c_buffer_info(stardata, buffer, nbytes);
+
+ /* get error buffer pointer */
+ binary_c_error_buffer(stardata, error_buffer);
+
+ /* free stardata (except the buffer) */
+ binary_c_free_memory(&stardata, // Stardata
+ TRUE, // free_preferences
+ TRUE, // free_stardata
+ TRUE, // free_store
+ FALSE, // free_raw_buffer
+ TRUE // free_persistent
+ );
+
+ return 0;
+}
+
+/* =================================================================== */
+/* Functions set up memoery adresses */
+/* =================================================================== */
+
+long int return_store_memaddr(char ** const buffer,
+ char ** const error_buffer,
+ size_t * const nbytes)
+{
+ struct libbinary_c_stardata_t * stardata = NULL;
+ struct libbinary_c_store_t * store = NULL;
+ char * empty_str = "";
+
+ /* Set up new system */
+ binary_c_new_system(&stardata, // stardata
+ NULL, // previous_stardatas
+ NULL, // preferences
+ &store, // store
+ NULL, // persistent_data
+ &empty_str, // argv
+ -1 // argc
+ );
+
+ /* output to strings */
+ // stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
+ // stardata->preferences->batchmode = BATCHMODE_LIBRARY;
+
+ /* get buffer pointer */
+ binary_c_buffer_info(stardata, buffer, nbytes);
+
+ /* get error buffer pointer */
+ binary_c_error_buffer(stardata, error_buffer);
+
+ /* free stardata (except the buffer) */
+ binary_c_free_memory(&stardata, // Stardata
+ TRUE, // free_preferences
+ TRUE, // free_stardata
+ FALSE, // free_store
+ FALSE, // free_raw_buffer
+ TRUE // free_persistent
+ );
+
+ /* convert the pointer */
+ uintptr_t store_memaddr_int = (uintptr_t)store; // C Version converting ptr to int
+ debug_printf("store is at address: %p store_memaddr_int: %ld\n", (void*)&store, store_memaddr_int);
+
+ /* Return the memaddr as an int */
+ return store_memaddr_int;
+}
+
+
+long int return_persistent_data_memaddr(char ** const buffer,
+ char ** const error_buffer,
+ size_t * const nbytes)
+{
+ /* Function to allocate the persistent_data_memaddr */
+ struct libbinary_c_stardata_t *stardata = NULL;
+ struct libbinary_c_store_t * store = NULL;
+ struct libbinary_c_persistent_data_t * persistent_data = NULL;
+ char * empty_str = "";
+
+ /* Set up new system */
+ binary_c_new_system(&stardata, // stardata
+ NULL, // previous_stardatas
+ NULL, // preferences
+ &store, // store
+ &persistent_data, // persistent_data
+ &empty_str, // argv
+ -1 // argc
+ );
+
+ /* get buffer pointer */
+ binary_c_buffer_info(stardata, buffer, nbytes);
+
+ /* get error buffer pointer */
+ binary_c_error_buffer(stardata, error_buffer);
+
+ /* convert the pointer */
+ uintptr_t persistent_data_memaddr_int = (uintptr_t)stardata->persistent_data; // C Version converting ptr to int
+ debug_printf("persistent_data is at address: %p persistent_data_memaddr_int: %ld\n", (void*)&stardata->persistent_data, persistent_data_memaddr_int);
+
+ /* free stardata (except the buffer) */
+ binary_c_free_memory(&stardata, // Stardata
+ TRUE, // free_preferences
+ TRUE, // free_stardata
+ TRUE, // free_store
+ FALSE, // free_raw_buffer
+ FALSE // free_persistent
+ );
+
+ /* Return the memaddr as an int */
+ return persistent_data_memaddr_int;
+}
+
+/* =================================================================== */
+/* Functions free memory */
+/* =================================================================== */
+
+int free_persistent_data_memaddr_and_return_json_output(long int persistent_data_memaddr,
+ char ** const buffer,
+ char ** const error_buffer,
+ size_t * const nbytes)
+{
+ struct libbinary_c_store_t *store = NULL;
+ struct libbinary_c_stardata_t *stardata = NULL;
+ char * empty_str = "";
+
+ // persistent_data:
+ struct libbinary_c_persistent_data_t *persistent_data;
+ if(persistent_data_memaddr != -1)
+ {
+ // load the persistent data from the long int that has been passed
+ persistent_data = (void*)persistent_data_memaddr;
+ debug_printf("Took long int memaddr %ld and loaded it to %p\n", persistent_data_memaddr, (void*)&persistent_data);
+ }
+ else
+ {
+ printf("ERROR: this function needs a valid persistent_data_memaddr value. not -1\n");
+ // persistent_data = NULL;
+ // TODO: put break in the function here.
+ }
+
+ /* Set up new system */
+ binary_c_new_system(&stardata, // stardata
+ NULL, // previous_stardatas
+ NULL, // preferences
+ &store, // store
+ &persistent_data, // persistent_data
+ &empty_str, // argv
+ -1 // argc
+ );
+
+ /* output to strings */
+ stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
+ stardata->preferences->batchmode = BATCHMODE_LIBRARY;
+
+ /* get output and free memory */
+ binary_c_output_to_json(stardata);
+
+ /* get buffer pointer */
+ binary_c_buffer_info(stardata, buffer, nbytes);
+
+ /* get error buffer pointer */
+ binary_c_error_buffer(stardata, error_buffer);
+
+ /* free the reststardata (except the buffer) */
+ binary_c_free_memory(&stardata, // Stardata
+ TRUE, // free_preferences
+ TRUE, // free_stardata
+ TRUE, // free_store
+ FALSE, // free_raw_buffer
+ FALSE // free_persistent
+ );
+
+ return 0;
+}
+
+int free_store_memaddr(long int store_memaddr,
+ char ** const buffer,
+ char ** const error_buffer,
+ size_t * const nbytes)
+{
+ struct libbinary_c_stardata_t *stardata = NULL;
+ struct libbinary_c_persistent_data_t *persistent_data = NULL;
+ char * empty_str = "";
+
+ // Store:
+ /* Check the value of the store_memaddr */
+ struct libbinary_c_store_t *store;
+ if(store_memaddr != -1)
+ {
+ // load the store from the integer that has been passed
+ store = (void*)store_memaddr;
+ debug_printf("Took long int store_memaddr %ld and loaded it to %p\n", store_memaddr, (void*)&store);
+ }
+ else
+ {
+ store = NULL;
+ }
+
+ /* Set up new system */
+ binary_c_new_system(&stardata, // stardata
+ NULL, // previous_stardatas
+ NULL, // preferences
+ &store, // store
+ &persistent_data, // persistent_data
+ &empty_str, // argv
+ -1 // argc
+ );
+
+ printf("freed store memaddr\n");
+ /* output to strings */
+ stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
+ stardata->preferences->batchmode = BATCHMODE_LIBRARY;
+
+ /* get buffer pointer */
+ binary_c_buffer_info(stardata, buffer, nbytes);
+
+ /* get error buffer pointer */
+ binary_c_error_buffer(stardata, error_buffer);
+
+ /* free the reststardata (except the buffer) */
+ binary_c_free_memory(&stardata, // Stardata
+ TRUE, // free_preferences
+ TRUE, // free_stardata
+ TRUE, // free_store
+ FALSE, // free_raw_buffer
+ TRUE // free_persistent
+ );
+
+ return 0;
+}